Innovative Genomic Medicine

The Genomics Sequencing Core at the Houston Methodist Research Institute operates a core facility that is devoted to helping researchers and clinicians stay on top of sequencing trends. The genomic sequencing facility includes equipment for the processing of samples for Illumina and Ion Torrent sequencing analysis as well as Illumina bead array analysis.

This equipment now includes an Ion Torrent Personal Genome Machine (PGM), capable of producing whole-genome-scale sequence data in a single-day run cycle, as well as a Genome Analyzer IIx, which regularly produces in excess of 3.5 gigabases of sequence information per week-long sequencing run. This equipment has been used for the sequencing of genomic DNA, Chromatin-IP DNA samples (ChIP-Seq), RNA samples (RNA-seq), microRNA and samples derived from novel experimental approaches. Supporting equipment includes an Illumina Cluster Station and a PCR workstation for the processing of samples. We use an Eppendorf Epmotion 5075 robotics system for the automated processing of samples. Our laboratory also has three real-time PCR machines (two Roche LightCycler 480 II and one Applied Biosystems 7900HT) for individual gene expression analysis.

Current Innovations in Genomic Medicine

Metabolomics: The central emphasis of our lab is the study of the mechanisms by which genetic and epigenetic changes alter the metabolic profile of individuals, and the ways in which these processes can lead to metabolic disease states. We are specifically interested in the mechanisms of action of nuclear hormone receptors, including thyroid receptor and PPARgamma. To this end, we have used ChIP-Seq and RNA-seq to examine these mechanisms on a genome-wide scale.

Mechanisms of Cancer Initiation: Most current models attribute cancer initiation to genetic or epigenetic events. However, years of investigation have demonstrated that these events are often complex and cryptic in nature. Genome-wide techniques provide us with a new method with which to study these events on a global scale. The projects at the Peak Center have provided new insight into these initiating events, using RNAseq and related techniques.

Pathogen Genomics: Next-generation sequencing techniques have provided a valuable tool for the genomic analysis of unicellular pathogens. The Peak Center has used such sequencing strategies to successfully investigate outbreaks and demonstrate the utility of such approaches as novel diagnostic tools for their analysis.

Genomic Drug Profiling: Whole-genome analysis techniques have provided a valuable set of tools to investigate the effects of novel drugs on a genome-wide scale. Our lab has pioneered the use of ChiP-Seq, RNA-seq and array-based methodologies to specifically investigate the effects of novel drugs on a genome-wide scale. We are currently pursuing these techniques to determine the effects of novel therapeutic compounds in the activation of specific gene profiles and with distinct, tissue-specific expression patterns.